Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structured”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex

The 22nd genetically encoded amino acid, pyrrolysine, plays a unique role in the key step in the growth of methanogens on mono-, di-, and tri-methylamines by activating the methyl group of these substrates for transfer to a corrinoid cofactor. Previous crystal structures of the Methanosarcina barkeri monomethylamine methyltransferase elucidated the structure of pyrrolysine and provide insight into its role in monomethylamine activation. Herein, we report the second structure of a pyrrolysine-containing protein, the M. barkeri trimethylamine methyltransferase MttB, and its structure bound to sulfite, a substrate analog of trimethylamine. We also report the structure of MttB in complex with its cognate corrinoid protein MttC, which specifically receives the methyl group from the pyrrolysine-activated trimethylamine substrate during methanogenesis. Together these structures provide key insights into the role of pyrrolysine in methyl group transfer from trimethylamine to the corrinoid cofactor in MttC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers

Polyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A deep generative model enables automated structure elucidation of novel psychoactive substances

Over the past decade, the illicit drug market has been reshaped by the proliferation of clandestinely produced designer drugs. These agents, referred to as new psychoactive substances (NPSs), are designed to mimic the physiological actions of better-known drugs of abuse while skirting drug control laws. The public health burden of NPS abuse obliges toxicological, police and customs laboratories to screen for them in law enforcement seizures and biological samples. However, the identification of emerging NPSs is challenging due to the chemical diversity of these substances and the fleeting nature of their appearance on the illicit market. Here, in this study, we present DarkNPS, a deep learning-enabled approach to automatically elucidate the structures of unidentified designer drugs using only mass spectrometric data. Our method employs a deep generative model to learn a statistical probability distribution over unobserved structures, which we term the structural prior. We show that the structural prior allows DarkNPS to elucidate the exact chemical structure of an unidentified NPS with an accuracy of 51% and a top-10 accuracy of 86%. Our generative approach has the potential to enable de novo structure elucidation for other types of small molecules that are routinely analysed by mass spectrometry.

Cheminformatics↗
DOE OSTI2020

Stabilizing the crystal structures of NaFePO 4 with Li substitutions

Due to the high cost and insufficient resources of lithium, alternative sodium-ion batteries have been widely investigated for large-scale applications. NaFePO 4 has the highest theoretical capacity of 154 mA h g -1 among the iron-based phosphates, which makes it an attractive cathode material for Na-ion batteries. Experimentally, LiFePO 4 has been highly successful as a cathode material in Li-ion batteries because its olivine crystal structure provides a stable framework during battery cycling. In NaFePO 4 , maricite replaces olivine as the most stable phase. However, the maricite phase is experimentally found to be electrochemically inactive under normal battery operating voltages (0–4.5 V). We found that partial substitutions of Na with Li stabilize the olivine structure and may be a way to improve the performance of NaFePO 4 cathodes. Using the previously developed structural LiFePO 4 database, here we examine the low-energy crystal structures in the system when we replace Li with Na. The known maricite and olivine NaFePO 4 phases are reconfirmed and an unreported phase with energy between them is identified by our calculations. Besides, the Li-doped olivine type compound Li x Na 1- x FePO 4 with mixed alkali ions retains better energetic stability compared with the other two types of structures of the same composition, as long as the proportion of Li exceeds 0.25. The thermodynamic stability of o-type Li x Na 1- x FePO 4 can be further improved at finite temperatures. The primary limitation of the calculations is that we mainly focus on the zero-temperature condition; however, the relative stability of the structures may vary depending on the ambient temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Combinatorial screening of crystal structure in Ba-Sr-Mn-Ce perovskite oxides with ABO 3 stoichiometry

ABO 3 oxides with the perovskite-related structures are attracting significant interest due to their promising physical and chemical properties for many applications requiring tunable chemistry, including fuel cells, catalysis, and electrochemical water splitting. Here we report on the crystal structure of the entire family of perovskite oxides with ABO 3 stoichiometry, where A and B are Ba, Sr, Mn, Ce. Given the vast size of this chemically complex material system, exploration for stable perovskite-related structures with respect to its constituent elements and annealing temperature is performed by combinatorial pulsed laser deposition and spatially-resolved characterization of composition and structure. As a result of this high-throughput experimental study, we identify hexagonal perovskite-related polytypic transformation as a function of composition in the Ba 1-x Sr x MnO 3 oxides after annealing at different temperatures. Furthermore, a hexagonal perovskite-related polytype is observed in a narrow composition-temperature range of the Ba 1-x Sr x MnO 3 oxides. In contrast, a tetragonally-distorted perovskite is observed across a wider range of compositions and annealing temperatures in the Sr 1-x Ce x MnO 3 oxides. This structure stability is further enhanced along the Ba 1-x Sr x MnO 3 - Sr 1-x Ce x MnO 3 pseudo-binary tie-line at x=0.25 by increasing Ba-incorporation and annealing temperature. These results indicate that the BaCe x Mn 1-x O 3 - Sr 1-x Ce x MnO 3 pseudo-binary oxide alloys (solid solutions) with tetragonal perovskite structure and broad composition-temperature range of stability are promising candidates for thermochemical water splitting applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Tailoring the structure and electrochemical performance of sodium titanate anodes by post-synthesis heating

Sodium titanate anodes synthesized via “chimie-douce” methods generally require a post-synthesis dehydration step. Their crystal structures are sensitive to the heating conditions such as temperature, resulting in distinct sodium storage performance. Herein, using in situ and ex situ high-temperature X-ray diffraction, we studied in detail the structural changes of Na 0.74 Ti 1.815 $\square$ 0.185 O 4 ·1.27H 2 O (NTO) under various heating conditions. Electrochemical characterization revealed that NTOs heated at lower temperatures with layered structures deliver larger capacities than those heated at high temperatures with tunnel structures. Heat treatment at moderate temperatures greatly improves the capacity retention of NTO, especially stabilizing the high voltage processes that are major contributors to the capacity fading, because of the modified crystal structure and surface chemistry. As a result, our findings suggest that post-synthesis heating is a simple and effective strategy to tailor the crystal structure, surface chemistry, and electrochemical properties of sodium titanate anodes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Critical fluctuations in liquid–liquid extraction organic phases controlled by extractant and diluent molecular structure

Extractant aggregation in liquid–liquid extraction organic phases impacts extraction energetics and is related to the deleterious efficiency-limiting liquid–liquid phase transition known as third phase formation. Using small angle X-ray scattering, we find that structural heterogeneities across a wide range of compositions in binary mixtures of malonamide extractants and alkane diluents are well described by Ornstein–Zernike scattering. This suggests that structure in these simplified organic phases originates from the critical point associated with the liquid–liquid phase transition. To confirm this, we measure the temperature dependence of the organic phase structure, finding critical exponents consistent with the 3D Ising model. Molecular dynamics simulations were also consistent with this mechanism for extractant aggregation. Due to the absence of water or any other polar solutes required to form reverse-micellar-like nanostructures, these fluctuations are inherent to the binary extractant/diluent mixture. Further, we also show how the molecular structure of the extractant and diluent modulate these critical concentration fluctuations by shifting the critical temperature: critical fluctuations are suppressed by increasing extractant alkyl tail lengths or decreasing diluent alkyl chain lengths. This is consistent with how extractant and diluent molecular structure are known to impact metal and acid loading capacity in many-component LLE organic phases, suggesting phase behavior of practical systems may be effectively studied in simplified organic phases. Overall, the explicit connection between molecular structure, aggregation and phase behavior demonstrated here will enable the design of more efficient separations processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Small angle X-ray studies of short-range order in non-stoichiometric pseudoprotic ionic liquids: the influence of chemical structure

Mixtures of organic acids and amines have been studied extensively owing to their unusual physicochemical properties and applications as solvents for extraction. In equimolar ratios they represent pseudoprotic ionic liquids, and in other, “nonstoichiometric” ratios they display a range of odd physicochemical behaviors. We report the results of small-angle X-ray scattering studies of a series of such systems with a range of chemical structures chosen to explore the link between molecular geometry and the character of the emergent nanoscale local liquid structure. We find that while the details vary, structure can emerge even when the hydrogen-bonding character of the components is changed significantly, and the character of their hydrocarbon substituents is altered. The consistent emergence of local order in the face of varying chemical structures indicates that the process is robust. Furthermore, this implies that the emergence of such structure may in fact be far more common in liquid mixtures than is currently recognized, and a great many structures may be suitable for the synthesis of pseudoprotic ionic liquids.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Structural and biochemical characterisation of Co 2+ -binding sites on serum albumins and their interplay with fatty acids

Serum albumin–Co 2+ interactions are of clinical importance. They play a role in mediating the physiological effects associated with cobalt toxicity and are central to the albumin cobalt binding (ACB) assay for diagnosis of myocardial ischemia. To further understand these processes, a deeper understanding of albumin–Co 2+ interactions is required. Here, we present the first crystallographic structures of human serum albumin (HSA; three structures) and equine serum albumin (ESA; one structure) in complex with Co 2+ . Amongst a total of sixteen sites bearing a cobalt ion across the structures, two locations were prominent, and they relate to metal-binding sites A and B. Site-directed mutagenesis and isothermal titration calorimetry (ITC) were employed to characterise sites on HSA. The results indicate that His9 and His67 contribute to the primary (putatively corresponding to site B) and secondary Co 2+ -binding sites (site A), respectively. The presence of additional multiple weak-affinity Co 2+ binding sites on HSA was also supported by ITC studies. Furthermore, addition of 5 molar equivalents of the non-esterified fatty acid palmitate (C16:0) reduced the Co 2+ -binding affinity at both sites A and B. The presence of bound myristate (C14:0) in the HSA crystal structures provided insight into the fatty acid-mediated structural changes that diminish the affinity of the protein toward Co 2+ . Together, these data provide further support for the idea that ischemia-modified albumin corresponds to albumin with excessive fatty-acid loading. Collectively, our findings provide a comprehensive understanding of the molecular underpinnings governing Co 2+ binding to serum albumin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Elucidating metal–organic framework structures using synchrotron serial crystallography

Metal organic frameworks (MOFs) are porous crystalline materials that display a wide variety of physical and chemical properties. Their single crystal structure determination is often challenging because in most cases micro- or nano-sized crystals spontaneously form upon MOF synthesis, which cannot be recrystallized. The production of larger single crystals for structure determination involves optimizing, and thus modifying, the conditions of synthesis, in which success cannot be guaranteed. Failure to produce crystals suitable for single-crystal X-ray diffraction leaves the 3D structure of the MOF compound unknown, and scientists must resort to more challenging structure solution methods based on X-ray powder or electron diffraction data. These laborious tasks can be avoided by using serial crystallography techniques which merge data collected on many micro-crystals. Here, we report the application of three synchrotron serial crystallography methods. We call these “mesh”, “grid” and “mesh&collect” scans. “Still” images (no rotation) are collected in the mesh scan approach, whereas small rotational wedges are collected in the grid scan method. The third protocol, mesh&collect, combines the acquisition of still images and rotational wedges. Using these means, we determine the ab initio structure of benchmark MOFs, MIL-100(Fe) and ZIF-8, that differ largely in unit cell size. These methods are expected to be widely applicable and facilitate structure determination of many MOF microcrystalline systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Synthesis, structure, and stability of a novel 2 H -azirine under pressure

We have synthesized 2,3-diphenyl-2H-azirine, a strained unsaturated heterocyclic compound, and examined its high-pressure behavior to above 10 GPa using diamond anvil cell techniques. Single crystal X-ray diffraction at ambient conditions reveals that the crystal structure is hexagonal and consists of interesting helices surrounding voids in the structure. A continuous shift of the Raman and infrared vibrational spectra with increasing pressure is observed, indicating that the molecular structure is preserved to at least 8 GPa at room temperature. High-pressure synchrotron powder X-ray diffraction shows that the hexagonal structure persists, with a smooth compression of the a and c parameters to 10 GPa. The structural stability under pressure is attributed to the reduction in void size within the helical framework despite the inherent strain and reactivity of the molecule. The channels in the structure could encapsulate small molecules for gas or energy storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Unveiling the role of structural vacancies in Mn-based Prussian blue analogues for energy storage applications

Prussian blue analogues (PBAs) are promising cathode materials for monovalent- and multivalent-ion batteries due to their large framework structures. Nevertheless, the influence of lattice vacancies on their electrochemical performance has not been thoroughly clarified, hindering the further development of PBAs. Here we identify two types of functional vacancies, i.e., structural vacancies (SVs) and incidental vacancies (IVs), in manganese hexacyanoferrate (MnHCF) through synchrotron-based X-ray absorption spectroscopy and density functional theory calculations. Unlike structurally disordered IVs, the introduction of structurally ordered SVs promotes ion transport and reduces the interaction between host ions and the framework, enabling improved cycling and rate performance. The controllable adjustment of SVs in K-rich MnHCF is achieved through a co-reactant method. Furthermore, the partial introduction of SVs in K-rich MnHCF is demonstrated to favor both a milder structural evolution by alleviating the Jahn–Teller distortion of Mn 3+ and a stable dynamic process of interface reaction. As a result, this study unveils the potential importance of incorporating structural vacancies into MnHCF for advanced energy storage applications.

Gao, Chongwei↗
DOE OSTI2024

Effect of solvothermal synthesis parameters on the crystallite size and atomic structure of cobalt iron oxide nanoparticles

We here investigate how the synthesis method affects the crystallite size and atomic structure of cobalt iron oxide nanoparticles. By using a simple solvothermal method, we first synthesized cobalt ferrite nanoparticles of ca. 2 and 7 nm, characterized by Transmission Electron Microscopy (TEM), Small Angle X-ray scattering (SAXS), X-ray and neutron total scattering. The smallest particle size corresponds to only a few spinel unit cells. Nevertheless, Pair Distribution Function (PDF) analysis of X-ray and neutron total scattering data shows that the atomic structure, even in the smallest nanoparticles, is well described by the spinel structure, although with significant disorder and a contraction of the unit cell parameter. These effects can be explained by the surface oxidation of the small nanoparticles, which is confirmed by X-ray near edge absorption spectroscopy (XANES). Neutron total scattering data and PDF analysis reveal a higher degree of inversion in the spinel structure of the smallest nanoparticles. Neutron total scattering data also allow magnetic PDF (mPDF) analysis, which shows that the ferrimagnetic domains correspond to ca. 80% of the crystallite size in the larger particles. A similar but less well-defined magnetic ordering was observed for the smallest nanoparticles. Finally, we used a co-precipitation synthesis method at room temperature to synthesize ferrite nanoparticles similar in size to the smallest crystallites synthesized by the solvothermal method. Structural analysis with PDF demonstrates that the ferrite nanoparticles synthesized via this method exhibit a significantly more defective structure compared to those synthesized via a solvothermal method.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Curiosity driven exploration to optimize structure–property learning in microscopy

Rapidly determining structure–property correlations in materials is an important challenge in better understanding fundamental mechanisms and greatly assists in materials design. In microscopy, imaging data provides a direct measurement of the local structure, while spectroscopic measurements provide relevant functional property information. Deep kernel active learning approaches have been utilized to rapidly map local structure to functional properties in microscopy experiments, but are computationally expensive for multi-dimensional and correlated output spaces. Here, we present an alternative lightweight curiosity algorithm which actively samples regions with unexplored structure–property relations, utilizing a deep-learning based surrogate model for error prediction. We show that the algorithm outperforms random sampling for predicting properties from structures, and provides a convenient tool for efficient mapping of structure–property relationships in materials science.

36 MATERIALS SCIENCE↗
DOE OSTI2026

A new layered kagome strip structure Na 2 Co 3 (AsO 4 ) 2 (OH) 2 : static and dynamic magnetic properties

One-dimensional kagome strip chains share much of the same frustrated structural motif as two-dimensional kagome antiferromagnets, making them valuable for deepening our understanding of kagome lattice magnetism. In this paper, we report the hydrothermal synthesis and detailed structural and property characterization of Na 2 Co 3 (AsO 4 ) 2 (OH) 2 , a striped kagome system. The crystal structure was characterized using single crystal X-ray diffraction which reveals that Na 2 Co 3 (AsO 4 ) 2 (OH) 2 crystallizes in monoclinic crystal system C2/m. The structure features a one-dimensional kagome strip lattice built from Co 2+ ions and undergoes an antiferromagnetic transition at T N = 14 K. The magnetic ground state at zero field was characterized using neutron powder diffraction. Below the magnetic transition, Na 2 Co 3 (AsO 4 ) 2 (OH) 2 orders into an antiferromagnetic structure with a k-vector (0.5, 0.5, 0.5). In the proposed model, the Co1 moment is predominantly confined to the ac-plane while the Co2 moment is primarily aligned along the b-axis. Two flat bands were observed in the inelastic neutron spectra below the magnetic transition, 5 and 10 meV. Inelastic neutron spectra were modeled with a Heisenberg Hamiltonian including three nearest-neighbor exchange interactions (J 1 , J 2 , J 3 ) and strong single-ion anisotropy to stabilize the observed magnetic structure. Our study highlights the complexity of Co 2+ -based kagome strip magnetic lattice compound Na 2 Co 3 (AsO 4 ) 2 (OH) 2 which provides an excellent platform to broaden our understanding of the frustrated kagome magnetic lattice space.

Liurukara, Duminda S. [Oak Ridge National Laborato↗
DOE OSTI2025

Structural incorporation into goethite fractionates rare earth elements

Up to 20% of rare earth elements (REEs) in ion adsorption deposits (IADs) are associated with iron oxide minerals, primarily goethite. Often termed “non-extractable”, goethite-hosted REEs are thought to be structurally incorporated into the mineral lattice. The large mismatch in size and charge density between REEs (ionic radius, r = 0.86–1.03 Å) and Fe 3+ (r = 0.65 Å), however, makes direct substitution energetically unfavorable. To determine REE compatibility with and incorporation into goethite on the atomic level, we used X-ray pair distribution function analysis (PDF) and LIII-edge extended X-ray absorption fine structure (EXAFS) spectroscopy. The compatibility of REEs with goethite and the precursor ferrihydrite (FH) is Lu ≥ Yb ≫ Dy > Nd for both phases. Nd and Dy primarily form secondary amorphous phases, with <30% Nd and Dy incorporated into goethite. In the FH precursor at pH 6.8, Yb and Lu assumed a local REE-OOH like structure with next nearest neighbor Fe. The Yb, Lu, and Nd-FH samples were also matured at ambient conditions for 100 days; despite the presence of only ∼5% goethite, Lu and Yb were 42% and 100% in goethite-like structural environments, respectively, whereas the PDF and EXAFS of Nd showed little evidence of any incorporation. Using ab initio molecular dynamics (AIMD) to model the EXAFS, we determined the presence of protonated Fe vacancies, edge-sharing with structural Lu and Yb, likely helped accommodate these REEs in the goethite structure. Incorporation into Fe oxyhydroxides thus potentially fractionates the REEs during weathering associated with formation of lateritic and ion adsorption deposits.

Mergelsberg, Sebastian T. [Pacific Northwest Natio↗
DOE OSTI2025

Understanding the structure and mechanism of Na + diffusion in NASICON solid-state electrolytes and the effect of Sc- and Al/Y-substitution

NASICON (sodium superionic conductor) based ceramics are one of the most promising classes of solid-state electrolytes for all-solid-state batteries. However, the mechanism of sodium ion diffusion is not understood in great detail since there is still a discrepancy between reported average structure models, local structures, and the number and position of sodium sites. To close this gap, we investigate the underlying diffusion mechanism and structural changes governing the Na + transport in Na 3.4 Zr 2 Si 2.4 P 0.6 O 12 using quasielastic neutron scattering (QENS) and powder X-ray diffraction (XRD). In the temperature range from 298 K to 640 K, the correlations between structural changes of a monoclinic C2/c to rhombohedral R $\bar{3}$c phase transition and the result of ion diffusion are investigated. The analysis of the quasielastic neutron scattering data reveals two quasielastic components corresponding to the Chudley-Elliott jump-diffusion model. It clearly shows two different Na + diffusion processes, local and long-range, on two different time and length scales and allows calculations of their corresponding activation energies. Additionally, the effects of Sc 3+ and Al 3+ /Y 3+ aliovalent substitution of Zr 4+ ions on the crystal structure and Na + diffusion are also studied. We can distinguish a local, chain, and cross-chain diffusion mechanism based on correlated QENS and XRD comparison of relevant nearest crystallographic Na–Na distances. The results reveal that the Na + diffusion in these NASICONs is three-dimensional and can provide guidelines on how dopants and changes in the crystal structure can affect the Na + conductivity.

25 ENERGY STORAGE↗
DOE OSTI2025

Electrosome assembly: Structural insights from high voltage-activated calcium channel (CaV)–chaperone interactions

Ion channels are multicomponent complexes (termed here as“electrosomes”) that conduct the bioelectrical signals required for life. It has been appreciated for decades that assembly is critical for proper channel function, but knowledge of the factors that undergird this important process has been lacking. Although there are now exemplar structures of representatives of most major ion channel classes, there has been no direct structural information to inform how these complicated, multipart complexes are put together or whether they interact with chaperone proteins that aid in their assembly. Recent structural characterization of a complex of the endoplasmic membrane protein complex (EMC) chaperone and a voltage-gated calcium channel (CaV) assembly intermediate comprising the pore-forming CaVα1 and cytoplasmic CaVβ subunits offers the first structural view into the assembly of a member of the largest ion channel class, the voltagegated ion channel (VGIC) superfamily. The structure shows how the EMC remodels the CaVα1/CaVβ complex through a set of rigid body movements for handoff to the extracellular CaVα2δ subunit to complete channel assembly in a process that involves intersubunit coordination of a divalent cation and ordering of CaVα1 elements. These findings set a new framework for deciphering the structural underpinnings of ion channel biogenesis that has implications for understanding channel function, how drugs and disease mutations act, and for investigating how other membrane proteins may engage the ubiquitous EMC chaperone.

Biochemistry & Molecular Biology↗